Alterations in composition and carbon biomass of phytoplankton community are closely related to seasonal variations, anthropogenic inputs and ultimately climatic changes in a longer perspective. Accuracy of the collected data is important to determine changes occurring in phytoplankton community composition. An intercomparison exercise of haptophyte abundance obtained by microscopy was performed by three research laboratories based on samples taken from 2 to 11 June 2016, in the western and central Black Sea. Total carbon biomass of phytoplankton groups was estimated by one of the three laboratories based on microscopy. Phytoplankton group composition was also determined with marker pigments. Carbon biomass of large sized diatoms and dinoflagellates was correlated with CHEMTAX derived chlorophyll a concentrations (Chl a) of these groups (r2=0.44-0.60, p<0.05). According to microscopy, carbon biomass of dinoflagellates was generally higher than that of diatoms and haptophytes, while based on HPLC-CHEMTAX analysis haptophytes and diatoms dominated in the region. Abundance of Emiliania huxleyi obtained by three laboratories were significantly different from each other (One way ANOVA) and abundance of only one of the laboratories was correlated with 19’-hexanoyloxyfucoxanthin concentration. Difference in abundance of this nanoplankton species among different laboratories appears to be related to both methodology in counting the cells and fixation of samples.